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Merged
bgruening merged 3 commits into from
Sep 15, 2016
Merged

Fastx 0.0.14 #942

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bf38d40
Add package_fastx_toolkit_0_0_14
mvdbeek Sep 15, 2016
2311571
Remove unused tags
mvdbeek Sep 15, 2016
2651db4
package_fastx_toolkit_0_0_14 also needs an update of package_libgtext…
mvdbeek Sep 15, 2016
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8 changes: 8 additions & 0 deletions packages/package_fastx_toolkit_0_0_14/.shed.yml
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categories:
- Tool Dependency Packages
description: Contains a tool dependency definition that downloads and compiles version
0.0.14 of the fastx toolkit.
name: package_fastx_toolkit_0_0_14
owner: iuc
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_fastx_toolkit_0_0_14
type: tool_dependency_definition
41 changes: 41 additions & 0 deletions packages/package_fastx_toolkit_0_0_14/tool_dependencies.xml
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<?xml version="1.0"?>
<tool_dependency>
<package name="libgtextutils" version="0.7">
<repository name="package_libgtextutils_0_7" owner="iuc" prior_installation_required="True" />
</package>
<package name="fastx_toolkit" version="0.0.14">
<install version="1.0">
<actions_group>
<actions architecture="x86_64" os="darwin">
<action type="download_by_url" sha256sum="9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806">https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2</action>
<action type="set_environment_for_install">
<repository name="package_libgtextutils_0_7" owner="iuc" prior_installation_required="True">
<package name="libgtextutils" version="0.7" />
</repository>
</action>
<action type="shell_command"><![CDATA[
CXXFLAGS="${CXXFLAGS} -std=c++11 -stdlib=libc++" &&
./configure --prefix=$INSTALL_DIR --disable-wall && make && make install ]]></action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>
<actions>
<action type="download_by_url" sha256sum="9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806">https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2</action>
<action type="set_environment_for_install">
<repository name="package_libgtextutils_0_7" owner="iuc" prior_installation_required="True">
<package name="libgtextutils" version="0.7" />
</repository>
</action>
<action type="autoconf">--disable-wall</action>
<action type="set_environment">
<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
</action>
</actions>
</actions_group>
</install>
<readme>
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
</readme>
</package>
</tool_dependency>
8 changes: 8 additions & 0 deletions packages/package_libgtextutils_0_7/.shed.yml
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categories:
- Tool Dependency Packages
description: Contains a tool dependency definition that downloads and compiles version
0.7 of the gtextutils libraries.
name: package_libgtextutils_0_7
owner: iuc
remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_libgtextutils_0_7
type: tool_dependency_definition
17 changes: 17 additions & 0 deletions packages/package_libgtextutils_0_7/tool_dependencies.xml
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<?xml version="1.0"?>
<tool_dependency>
<package name="libgtextutils" version="0.7">
<install version="1.0">
<actions>
<action type="download_by_url" sha256sum="792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a">https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz</action>
<!-- Some versions of GCC warn about a variable being set but not used, and fail due to -Werror -->
<action type="autoconf">--disable-wall</action>
<action type="set_environment">
<environment_variable name="PKG_CONFIG_PATH" action="prepend_to">$INSTALL_DIR/lib/pkgconfig</environment_variable>
</action>
</actions>
</install>
<readme>
</readme>
</package>
</tool_dependency>